Review Article

Diagnostic Options and Challenges for

Dengue and Chikungunya Viruses
Stacey K. Mardekian and Amity L. Roberts
Abstract
Dengue virus (DENV) and Chikungunya virus (CHIKV) are arboviruses that
share the same Aedes mosquito vectors and thus overlap in their endemic areas.
These two viruses also cause similar clinical presentations, especially in the initial
stages of infection, with neither virus possessing any specific distinguishing
clinical features. Because the outcomes and management strategies for these two
viruses are vastly different, early and accurate diagnosis is imperative. Diagnosis
is also important for surveillance, outbreak control, and research related to vaccine
and drug development. Available diagnostic tests are aimed at detection of the
virus, its antigenic components, or the host immune antibody response. In this
review, we describe the recent progress and continued challenges related to the
diagnosis of DENV and CHIKV infections.
1. Introduction

Dengue virus (DENV) and Chikungunya virus (CHIKV) are single-stranded,

positive-sense RNA viruses. DENV belongs to the family Flaviviridae and
genus Flavivirus of which there are 5 known serotypes (DENV15). CHIKV
belongs to the family Togaviridae and genus Alphavirus of which there are 3
known strains (Asian-West African; East-Central; South African) [1]. The genome

of each virus is approximately 11kb in length [ 1,2]. The DENV genome encodes
three structural (C, prM, and E) and seven nonstructural (NS1, NS2B, NS3,
NS4A, NS4B, and NS5) proteins [3]. The CHIKV genome encodes three
structural (C, E1, and E2) and four nonstructural (nsP14) proteins [1].
Both viruses are arthropod-borne viruses (arboviruses) sharing a common vector:
mosquitos of the Aedesgenus, specifically A. aegypti and A. albopictus [4]. Both
viruses circulate in similar geographic regions. In nonendemic regions, travelassociated infections are an important consideration for patients with a recent
travel history who present with fever. Concurrent infection with both viruses,
transmitted from either two different mosquitos or one dually infected mosquito,
is possible [5, 6]. For DENV, transmission has also been reported to occur via
infected blood products, organ donation, and prenatal and/or perinatal vertical
transmission [7].
While DENV and CHIKV present similarly as an acute febrile illness, these two
viruses have vastly different management strategies and outcomes. The majority
of CHIKV infections are self-limiting with chronic joint disease being the most
common long-term outcome, and fatality is exceedingly rare. Nonsteroidal antiinflammatory drugs (NSAIDs) are the mainstay treatment for CHIKV, but
NSAIDs should be avoided until DENV is confidently ruled out, as NSAIDs are
contraindicated in DENV infection [8]. DENV is likewise commonly a selflimiting illness, yet this diagnosis necessitates stricter monitoring due to the
potential for more significant morbidity and mortality. Infection with one serotype
of DENV confers lifelong immunity to that particular serotype but only short-term
immunity to the other serotypes; subsequent infections with a different serotype
increase the risk of severe complications [7].
2. Epidemiology

The majority of DENV and CHIKV infections affect people residing in endemic
areas, which include most of the tropical and subtropical regions in the world.

Many of these areas serve as popular tourist destinations and, consequently,

dengue-related infections have recently surpassed malaria and gastrointestinal
infections as the most common cause of fever among travelers [23]. The major
endemic regions include Southeast Asia, the Western Pacific, the Eastern
Mediterranean, Africa, and the Americas [9]. Specific countries with cocirculation
and coinfections of DENV and CHIKV include India, Sri Lanka, Gabon,
Cameroon, Madagascar, Indonesia, Singapore, and Thailand [24]. In the United
States, autochthonous outbreaks of DENV have been reported in Hawaii and
along the Texas-Mexico border, and outbreaks of both DENV and CHIKV have
recently occurred in southwest Florida [6, 25].

3. Clinical Presentation

These two viruses share a similar geographic distribution; unfortunately, their

clinical manifestations also show substantial overlap. The typical incubation
periods for DENV and CHIKV are 47 days and 37 days, respectively [4].
Patients infected with either virus typically present with acute onset of fever,
myalgia, and headache, and some patients experience a maculopapular rash and/or
gastrointestinal symptoms [4, 6].
A classification scheme for DENV, put forth by the World Health Organization
(WHO) in 2009, includes criteria for probable dengue and severe dengue [9].
Most DENV infections are either asymptomatic or mild and self-limited, but there
are warning signs that may suggest which patients may progress to severe
disease and require stricter medical management [9]. Severe dengue may manifest
as significant plasma leakage, hemorrhagic complications, and/or severe organ
impairment, so early recognition of DENV infection is imperative [9].
Compromising the sensitivity of the WHO classification scheme is the fact that
patient age influences the type and severity of symptoms; Low et al. found that

fewer older adults reported symptoms of myalgia and arthralgia, as well as

mucosal bleeding, which is one of the primary warning signs [26].
The clinical course for CHIKV is likewise typically mild and self-limited. The
hallmark presentation of CHIKV is a bilateral migratory arthralgia, often intense,
affecting mainly the small joints of the extremities [1, 4]. However, most children
with CHIKV report only mild arthralgia [8]. The major long-term complication is
persistence of joint pain and stiffness, which may last years after resolution of the
initial infection [1]. Rarely, CHIKV infection is associated with neurologic,
ophthalmologic, and hemorrhagic disease [4, 5].
While neither infection possesses a defining clinical feature, there are suggested
trends in the symptomatology and complete blood count (CBC) results that may
help differentiate between the two infectious processes. It is suggested that, at
initial presentation, significantly more DENV patients have thrombocytopenia
(platelets < 100 109/L) and associated minor bleeding complications such as
petechiae and nose bleeds, while patients with CHIKV are more likely to have
arthralgia. Leukopenia is common to both infections at initial presentation but
tends to be more pronounced in DENV patients; CHIKV patients tend to have
higher white blood cell (WBC) counts (>3.6 or 5.0 10 9/L according to two
separate authors) than DENV patients [4, 6, 8]. During the course of illness,
DENV patients are more likely to have abdominal pain and the CBC will
demonstrate leukopenia, neutropenia, and thrombocytopenia that is more frequent
and more pronounced than in CHIKV patients. In contrast, CHIKV patients may
show a shorter duration of fever, conjunctivitis, acute arthritis, and more
prominent arthralgia affecting multiple joints [6]. While these trends in clinical
findings may be helpful, they are neither specific nor consistent enough to be
considered diagnostic.
Unfortunately, there is no single clinical or laboratory marker available for
distinguishing DENV or CHIKV infection from each other or from other acute
febrile illnesses. Therefore, both of these viruses must be initially included in the

differential diagnosis for a patient with suspicious clinical symptoms who is living
in or returning from travel to an endemic area. Clinical features can serve, at best,
as a guide for favoring one virus over the other, as patients may present atypically,
either by lacking the classic signs or symptoms as mentioned above, or by
presenting in an uncharacteristic manner. Laboratory diagnostic tests are thus
essential for accurate identification of the causative virus.
4. Methods for Diagnosis

A wide variety of laboratory diagnostic methods are available to aid in the

diagnosis of DENV and CHIKV infections. The premise of these tests is detection
of the virus, viral components (antigens or nucleic acid), or the host immunologic
response to the virus [10]. Therefore, selection and interpretation of testing
depends on the kinetics of viremia and antibody response, which differ between
primary and secondary infections. Other factors influencing test choice include the
purpose of testing and availability of resources. Each type of test offers unique
advantages and disadvantages, and a combination of tests may be employed in
order to increase diagnostic confidence. For a summary of available tests for
DENV and CHIKV infection, see Tables 1 and 2, respectively.
4.1. Overview of Currently Available Tests
The acute febrile phase of infection corresponds to the period of viremia, which
lasts typically from 5 days after onset of fever for both DENV and CHIKV.
During this time, diagnosis rests on isolation of the virus, viral RNA, or viral
antigen from the specimen. Isolation of DENV or CHIKV can be performed via
mosquito inoculation or cell culture; CHIKV isolation can also be accomplished
by intracerebral inoculation of mice [16]. Virus may be recovered from serum,
plasma, whole blood, or tissues collected at autopsy. Mosquito inoculation is the
most sensitive isolation method but is impractical for routine diagnosis due to the
highly specialized requirements and high maintenance costs [3]. Cell culture is in
wider use, with preference given to the mosquito cell line C6/36 (cloned from A.

albopictus) or AP61 (cloned from A. pseudoscutellaris) [9, 16]. Other less

sensitive options include mammalian cell cultures such as Vero, LLC-MK2, and
BHK-21 [3]. The resultant virus isolate may be further characterized during
subsequent in vitro studies, such as genome sequencing, virus neutralization, and
infection studies [3]. Virus isolation is highly specific and has a theoretical
detection limit of a single viable virus, although, in practice, the sensitivity is only
approximately 40.5% in cell line-based virus isolation. It also requires highly
trained operators, a dependence on sample integrity and a short viremia period,
thus providing a narrow window of opportunity from illness onset. Virus isolation
followed by an immunofluorescence assay for confirmation requires days to
weeks [9, 16]. Therefore, despite its advantages, this approach is not widely used
in routine diagnostic laboratories and may serve more use in surveillance
purposes. A more recent development in viral isolation is described by Patramool
et al., who used anionic polymer-coated beads to isolate DENV and CHIKV [27].
This may prove a useful strategy to monitor the status of circulating mosquitos in
regions at risk for outbreaks with these arboviruses. Compared to traditional
isolation techniques, this method provides reduced cost, good sensitivity, and
rapidity, which is conducive to simultaneous analysis of a large number of
samples [27].
Compared to virus isolation, viral nucleic acid detection techniques performed on
acute-phase specimens offer better sensitivity with a much more rapid turnaround
time. Viral nucleic acid can be detected for a few additional days beyond the
period of viremia. Detection of viral nucleic acid can be accomplished by reverse
transcriptase polymerase chain reaction (RT-PCR), real time RT-PCR, or
isothermal amplification methods. All of these methods involve three basic steps:
viral RNA extraction, amplification, and detection and characterization of the
amplified product [9]. There is a wide variety of specimen types that can be tested
with RT-PCR, including blood, serum, plasma, and fresh or formalin-fixed
paraffin-embedded tissues. For DENV, urine and saliva have been found to be
suitable specimen types as well [3]. Testing urine samples by real-time RT-PCR

provides a larger window of detection that extends well past the viremia period;
DENV RNA may be detected in urine up to day 16, compared to day 8 for blood
specimens [28]. The ability to test urine and saliva is advantageous in patients for
whom blood samples are difficult to obtain, such as in newborns and patients with
hemorrhagic syndromes [14].
RT-PCR using primers designed for structural and nonstructural domains has been
found to be useful in the rapid diagnosis of CHIKV. The combination of RTPCR/nested PCR has proved efficient for specific detection and genotyping of
CHIKV. Loop-mediated isothermal amplification (LAMP) assays can be rapidly
carried out at a single temperature in a water bath, with visually detectable results,
and comparable sensitivities to conventional PCR [17].
Detection of viral antigens is another diagnostic methodology available for DENV
infection. Nonstructural protein 1 (NS1) antigen is a highly conserved
glycoprotein produced during the virus replication process, and a soluble form of
NS1 accumulates in high concentrations in the serum of patients with both
primary and secondary DENV infections [29, 30]. Several commercial assays,
consisting of both rapid tests and enzyme-linked immunosorbent assay (ELISA)
kits, are available for the detection of the NS1 antigen. Serum is the most common
sample type. DENV NS1 can also be detected in urine samples during the acute
phase of DENV infection, which provides an opportunity for the development of a
rapid noninvasive test [11]. Lastly, NS1 antigen may be detected in the
cerebrospinal fluid (CSF) of patients with neurological symptoms [12]. A
downfall is that these tests do not differentiate between dengue serotypes, as NS1
is highly conserved by all serotypes. Additionally, these tests are most successful
during the acute phase of illness and lose sensitivity once the period of viremia
ends. The sensitivity of NS1 has also been found to be lower in DENV secondary
infections, which is thought to be due to assay interference by anti-NS1 antibodies
which are present more frequently in secondary infections [10, 29]. An antigenbased commercial detection assay is not widely available for CHIKV, and the ones

described thus far in the literature have unclearly established performance

characteristics [21, 22].
After the period of viremia, the methods described thus far become much less
sensitive for diagnosis. At this point, the best diagnostic strategy entails detection
of antibodies indicative of host immune response to the virus. However, the caveat
is that individuals in endemic areas often have immunologic levels to these
viruses. Serologic methods include ELISA, indirect immunofluorescence assays
(IFA), hemagglutination inhibition (HI), and microneutralization (MNt) [1].
ELISA and IFA are rapid and sensitive techniques for detecting virus-specific
antibodies and can distinguish between IgG and IgM. For techniques that cannot
make this distinction (HI and MNt), it is required to compare paired serum
samples (acute and convalescent phases) to establish recent infection.
For DENV, serologic methods are most commonly employed, in particular IgM
capture ELISA [4]. IgM antibodies are detectable in 50% by days 35 after onset,
80% by day 5, and 99% by day 10 after initial symptoms. They may persist for
months; hence DENV IgM antibodies are a reliable marker of recent but not
necessarily acute infection [29]. IgG antibody response develops a few days after
the onset of IgM antibodies, and IgG may persist for many years [29]. Serologic
confirmation of infection requires demonstration of a fourfold rise in antibody
titer between acute and convalescent phase sera, or by demonstration of IgM
antibodies specific for the virus [16]. Patterns of antibody response differ between
primary and secondary infections, with primary dengue invoking stronger and
more specific IgM response than in secondary, which have stronger and more
rapid IgG response. Prior vaccination against other Flavivirus (Japanese
encephalitis virus; Yellow-fever virus) or prior infection with nondengue
flaviviruses (including West Nile) can potentially influence antibody responses
measured in some assays [4]. The recent introduction of rapid diagnostic kits that
offer combined detection of NS1 and IgM/IgG antibodies was an effort to create a
point-of-care test with better performance characteristics [13]. Evaluation of some

of these combined tests has revealed diagnostic sensitivity of 8993% and

specificity of 75100% [3, 13].
A combination of molecular and IgM antibody detection assays is recommended
for diagnosis of CHIKV infection. Some advocate adopting an algorithmic
approach, wherein the IgM capture ELISA is used as an initial screening tool
followed by the use of rapid molecular assays in CHIKV IgM negative samples,
to facilitate rapid diagnosis during outbreaks [18].
4.2. Simultaneous Testing for DENV and CHIKV
Because infection with DENV and CHIKV should be on the differential diagnosis
together at the initial patient presentation, tests that screen for these viruses
simultaneously are preferred to test for them separately. CHIKV and DENV are
not readily differentiated serologically due to cross-reactivity of their
serocomplexes, so there is a reliance on molecular detection methods for this
purpose [19]. A one-step duplex conventional RT-PCR assay for distinguishing
DENV and CHIKV has been reported [20]. Saha et al. developed a highly
sensitive and specific, rapid one-tube duplex RT-PCR assay which provides a
result within 110 minutes [19]. Two authors have described a one-step multiplex
real-time RT-PCR assay that can simultaneously detect and quantitate RNA for all
DENV serotypes and CHIKV. Cecilia et al. report a sensitivity of 100% for
DENV and 95.8% for CHIKV, while the specificity was 100% for both viruses
when compared to conventional RT-PCR [24]. Pongsiri et al. report an assay
sensitivity of 97.65% and specificity of 92.59% when compared to conventional
RT-PCR

[31].

Real-time

reverse

transcription-loop-mediated

isothermal

amplification (RT-LAMP) is a sensitive alternative to real-time PCR for use in

field applications [18]. A RT-LAMP method has been described in which a reverse
transcription and amplification was designed in one step with two tubes under the
same reaction conditions for the rapid identification and quantitative detection of
RNA for CHIKV and DENV, respectively [32]. This assay has a sensitivity of
100% and specificity of 95.25%. The LAMP reaction can be ended within one

hour under isothermal conditions and does not require sophisticated instruments,
making this method adaptive to field diagnosis. Additionally, the use of a
turbidimeter allows for quantitative detection of viral load [32]. For RT-PCR
assays described above, the one-step process reduces the chance of contamination
and there is lack of cross-reactivity between related Flavivirus groups and DENV
[19].
4.3. Sending Out Samples
Within the United States, CHIKV testing is performed at the Centers for Disease
Control and Prevention (CDC), a limited number of select state health
departments, and one commercial laboratory. The CDCs Arbovirus Diagnostic
Laboratory at the Division of Vector-Borne Diseases (DVBD) is located in Fort
Collins, CO. Test results are normally available 4 to 14 days after specimen
receipt, but reporting times may be longer during summer months when arbovirus
activity increases. Initial serological testing is performed using IgM capture
ELISA and IgG ELISA. If the initial results are positive, further confirmatory
testing is performed which may delay the reporting of final results. All results are
sent to the appropriate state health department.
The CDC Dengue Branch, located in San Juan, Puerto Rico, provides DENV
testing free of charge to submitting physicians and state and private laboratories.
A Dengue Case Investigation Form must accompany the specimen. One
potentially problematic issue with sending samples to this laboratory is that an
international shipping license is required. Another challenge, especially for
underdeveloped countries, is specimen preservation during shipment. The CDC
recommendation is that the serum specimen is frozen immediately after separation
and sent on dry ice, or alternatively kept refrigerated and sent in cold packs.

4.4. Future Test Developments

Other diagnostic methodologies may be available for future use in the laboratory
diagnosis of DENV and CHIKV infection. One technique becoming an
increasingly popular serological option in arbovirology is microsphere-based
immunoassay (MIA). This technology is based on detection by flow cytometry of
antigen or antibody attached to microspheres or beads. This is a much more rapid
test than MAC-ELISA and also has the potential for performance in multiplex
[33]. Similarly, microarray technology, which focuses on detection of nucleic acid
fragments corresponding to different pathogens, is useful to screen a sample for
the many pathogens on a wide differential diagnosis for infectious symptoms in a
given region [10]. Finally, mass spectrometry could be applied to this field of
diagnosis, proving especially useful in determining viral serotypes and genotypes
during an outbreak [9].
5. Conclusion

Confirmation of DENV or CHIKV infection requires laboratory diagnosis.

Molecular assays are more sensitive for diagnosis in the early stages of illness (2
5 days after onset) when antibodies are not detected. However, in the later stages
of illness, the sensitivity of molecular methods decreases due to the onset of a
brisk immune response and corresponding reduction in viral load. At this stage,
the IgM ELISA is a more sensitive diagnostic test.
An ideal diagnostic test meets certain key criteria: affordability by those at risk of
infection, specificity, sensitivity, ease of use, rapid results, little reliance on
equipment, and delivery to those in need [29]. The ideal test should also be part of
a multiplexed assay for other pathogens causing acute undifferentiated fever, such
as malaria [17]. Progress for DENV and CHIKV diagnostic testing has been
made. Generally, tests with high sensitivity and high specificity require more
complex technologies and technical expertise, while rapid tests may sacrifice
sensitivity and specificity for the advantages of speed and ease of performance. It

is difficult to find a balance between accessibility of a diagnostic method and the

confidence in the test results. Antigen detection assays seem most promising for
rapid and early diagnosis in rural areas. In this regard, development of DENV
diagnostic tests is ahead of those for CHIKV, but clearly both of these arboviruses
are important causes of disease in their shared endemic regions and in travelers to
these areas.
Conflict of Interests

The authors declare that there is no conflict of interests regarding the publication
of the paper.